Figure 5 | Scientific Reports

Figure 5

From: Computational Analysis of the Molecular Mechanism of RamR Mutations Contributing to Antimicrobial Resistance in Salmonella enterica

Figure 5

Analysis of the RamR-DNA binding free energy. (A) Thermodynamic cycle for binding affinity calculations. Distribution of the work values over time for an alchemical free energy simulation of (B) Y59H, (C) M84I, and (D) E160D mutations for the DNA-free (left panel) and DNA-bound (right panel) RamR proteins. The left plot in each result shows the work values obtained from the integration of \(\delta {H}_{\lambda }/\delta \lambda \) as a function of the sampling time of the equilibrium states. The right plot in each result shows the histograms of work values from which the free energy was calculated. (E) In addition, the binding free energies caused by mutations (\({\rm{\Delta }}{\rm{\Delta }}{G}_{bind}\)) were calculated.

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